Bottom Line:
Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature.We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes.These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations.

evv093-F2: Pairwise Fst values between Atlantic cod populations using 8,809 SNPs in 23 LGs. SNPs are ordered according to LG and position within LGs based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows that of Hubert et al. (2010). Median Fst estimates between the population pairs are denoted in parentheses.

Mentions:
Locus-specific FST values for all pairwise population comparisons indicate a genome-wide pattern of high FST when comparisons are made to the Baltic Sea, whereas few discrete regions of the genome show elevated FST values in the remaining comparisons (fig. 2). A total of 40 private alleles (supplementary table S2, Supplementary Material online) were detected among the populations, 38 of which were rare in frequency (<0.04). The highest number of private alleles (23) was observed in the North Sea population and the lowest number (3) was observed in the Baltic population. The two private alleles of higher frequency (0.179 and 0.232) were found in the North Sea population, in complete linkage disequilibrium (LD) with each other (ss1712302407 and ss1712304757, located 241 bp apart, in LG3). In total, 334 fixed allele frequencies were detected in any population; however, only 84 of these showed frequency differences of more than 0.1 in any pairwise comparison. Out of these, 59 were unique to the Baltic population (19 potentially under selection) whereas 11, 2 and 1 were unique to the North Sea, Kattegat and Öresund populations, respectively. In addition, 59 outlier SNPs were close to fixation (frequency > 0.95; supplementary table S2, Supplementary Material online).Fig. 2.—

evv093-F2: Pairwise Fst values between Atlantic cod populations using 8,809 SNPs in 23 LGs. SNPs are ordered according to LG and position within LGs based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows that of Hubert et al. (2010). Median Fst estimates between the population pairs are denoted in parentheses.

Mentions:
Locus-specific FST values for all pairwise population comparisons indicate a genome-wide pattern of high FST when comparisons are made to the Baltic Sea, whereas few discrete regions of the genome show elevated FST values in the remaining comparisons (fig. 2). A total of 40 private alleles (supplementary table S2, Supplementary Material online) were detected among the populations, 38 of which were rare in frequency (<0.04). The highest number of private alleles (23) was observed in the North Sea population and the lowest number (3) was observed in the Baltic population. The two private alleles of higher frequency (0.179 and 0.232) were found in the North Sea population, in complete linkage disequilibrium (LD) with each other (ss1712302407 and ss1712304757, located 241 bp apart, in LG3). In total, 334 fixed allele frequencies were detected in any population; however, only 84 of these showed frequency differences of more than 0.1 in any pairwise comparison. Out of these, 59 were unique to the Baltic population (19 potentially under selection) whereas 11, 2 and 1 were unique to the North Sea, Kattegat and Öresund populations, respectively. In addition, 59 outlier SNPs were close to fixation (frequency > 0.95; supplementary table S2, Supplementary Material online).Fig. 2.—

Bottom Line:
Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature.We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes.These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations.